EnglishFrenchSpanish

Ad


OnWorks favicon

bp_process_wormbasep - Online in the Cloud

Run bp_process_wormbasep in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bp_process_wormbasep that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


bp_process_wormbase.pl - Massage WormBase GFF files into a version suitable for the
Generic Genome Browser

SYNOPSIS


% bp_process_wormbase.pl ./WS61 > wormbase.gff

DESCRIPTION


This script massages the Wormbase GFF files located at
ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the GFF format suitable
for display by the generic genome browser. It mainly adds comments to the annotations and
designates certain well-spaced genetic loci as framework landmarks.

This script requires the AcePerl distribution, which is available on CPAN (look for the
"Ace" module).

To use this script, get the WormBase GFF files from the FTP site listed above and place
them in a directory. It might be a good idea to name the directory after the current
release, such as WS61. You do not need to uncompress the files.

Then give that directory as the argument to this script and capture the script's output to
a file:

% bp_process_wormbase.pl ./WS61 > wormbase.gff

It may take a while before you see output from this script, since it must first fetch gene
and protein database from the remote AceDB running at www.wormbase.org. The wormbase.gff
file can then be loaded into a Bio::DB::GFF database using the following command:

% bulk_load_gff.pl -d <databasename> wormbase.gff

Use bp_process_wormbasep online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    deep-clean
    deep-clean
    A Kotlin script that nukes all build
    caches from Gradle/Android projects.
    Useful when Gradle or the IDE let you
    down. The script has been tested on
    macOS, but ...
    Download deep-clean
  • 2
    Eclipse Checkstyle Plug-in
    Eclipse Checkstyle Plug-in
    The Eclipse Checkstyle plug-in
    integrates the Checkstyle Java code
    auditor into the Eclipse IDE. The
    plug-in provides real-time feedback to
    the user about viol...
    Download Eclipse Checkstyle Plug-in
  • 3
    AstrOrzPlayer
    AstrOrzPlayer
    AstrOrz Player is a free media player
    software, part based on WMP and VLC. The
    player is in a minimalist style, with
    more than ten theme colors, and can also
    b...
    Download AstrOrzPlayer
  • 4
    movistartv
    movistartv
    Kodi Movistar+ TV es un ADDON para XBMC/
    Kodi que permite disponer de un
    decodificador de los servicios IPTV de
    Movistar integrado en uno de los
    mediacenters ma...
    Download movistartv
  • 5
    Code::Blocks
    Code::Blocks
    Code::Blocks is a free, open-source,
    cross-platform C, C++ and Fortran IDE
    built to meet the most demanding needs
    of its users. It is designed to be very
    extens...
    Download Code::Blocks
  • 6
    Amidst
    Amidst
    Amidst or Advanced Minecraft Interface
    and Data/Structure Tracking is a tool to
    display an overview of a Minecraft
    world, without actually creating it. It
    can ...
    Download Amidst
  • More »

Linux commands

Ad